After minor repairs and system checkout, Boxer deployed to the Western Pacific from 24 March 1997 to 24 September 1997, along with Ogden and Fort Fisher, and visited many foreign ports of call.

Boxer deployed again to the Western Pacific, Persian Gulf and Red Sea on 14 March 2001 in support of Operation Southern Watch.

In 2003, as a result of the impending war and the need for troops in Iraq, Boxer found herself deploying yet again, this time six months ahead of schedule.

She delivered equipment and supplies to Kuwaiti Naval Base in the northern Persian Gulf for the continuing support of the post-war rebuilding of Iraq.

It was reported that the German department of defense influence and contacts to James Jones led to the U.S. decision to withdraw from the scene.

[8] The ship, with the 13th Marine Expeditionary Unit, departed San Diego on 22 February 2011 for a seven-month deployment in the Pacific and Indian Oceans.

[10][11][12] On 16 June 2016, Boxer, supported by amphibious warfare ships New Orleans and Harpers Ferry took part in Operation Inherent Resolve; AV-8BII Harriers of the 13th MEU flying off the ship began airstrikes against ISIL in Iraq and Syria, making it the first time the U.S. Navy used ship-based aircraft from both the Mediterranean and the Persian Gulf at the same time during the Operation[13] (aircraft from the aircraft carrier Harry S. Truman began airstrikes on ISIL targets from the Mediterranean on 3 June).

[14] On 18 July 2019, President Donald Trump stated that the ship shot down and destroyed an Iranian drone over the Strait of Hormuz.

[19] On 7 April 2020, it was reported that BAE systems had been awarded a contract from the US Navy to perform extensive modernization and maintenance to the USS Boxer, with work scheduled to commence in June 2020, and complete in around 18 months' time in December 2021.